A command line tool for visualizing CSV/spreadsheet-like data

Overview

PerfPlotter

pre-commit

Read data from CSV files using pandas and generate interactive plots using bokeh, which can then be embedded into HTML pages and served by server-client applications (or at least allow them to be viewed on a browser).

Contents

Environment

  • Python 3.8.x
  • macOS 10.15.x
  • Firefox 88.x

Setup

  1. Clone and cd into the perfplotter directory
  2. Install dependencies
    $ pipenv install --dev --python=/path/to/python3.8
    
    
  3. Install pre-commit hooks
    $ pre-commit install
    $ pre-commit run --all-files
    
    
    • Optional: pre-commit autoupdate
  4. Activate virtual environment
  5. In the same directory as setup.py, install *perfplotter as an editable dependency:
    $ pip install -e .
    
    
    • Use bare pip here to exclude perfplotter from the Pipfile* (which is under version control)
    • Do pipenv clean to really make sure it's not included in the Pipfile*
  6. Start and open any of the jupyter notebooks
    $ jupyter notebook --notebook-dir tutorials/notebooks
    
    

Usage

Show the main usage/help info

$ perfplotter --help

Show each command's usage/help info

$ perfplotter examples --help
$ perfplotter timeseries --help
$ perfplotter histogram --help

Supported plots

  • Plot TimeSeries
    $ perfplotter timeseries --help
    $ perfplotter timeseries /path/to/my.csv -x 1 -y 2
    
    
  • Plot Histogram
    $ perfplotter histogram --help
    $ perfplotter histogram /path/to/my.csv -x 1 -y 2
    
    

Use examples to test

$ perfplotter examples sample1
Generated 
   
    /out/sample1.csv

$ perfplotter timeseries out/sample1.csv

   

The last command should open up a browser with an interactive plot of sample1.csv

sample-timeseries-browser

Distribution

  1. In the same directory as setup.py:
    $ python setup.py sdist
    
    
    • This should create a dist/perfplotter-VERSION.tar.gz file
  2. In another directory (i.e. a test env) where perfplotter will be used:
    $ pipenv install /path/to/perfplotter/dist/perfplotter-VERSION.tar.gz
    
    
Comments
  • chore(deps): Bump notebook from 6.3.0 to 6.4.12

    chore(deps): Bump notebook from 6.3.0 to 6.4.12

    Bumps notebook from 6.3.0 to 6.4.12.

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    dependencies 
    opened by dependabot[bot] 1
  • chore(deps): Bump notebook from 6.3.0 to 6.4.10

    chore(deps): Bump notebook from 6.3.0 to 6.4.10

    Bumps notebook from 6.3.0 to 6.4.10.

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    dependencies 
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  • chore(deps): Bump jupyter-server from 1.6.4 to 1.15.4

    chore(deps): Bump jupyter-server from 1.6.4 to 1.15.4

    Bumps jupyter-server from 1.6.4 to 1.15.4.

    Release notes

    Sourced from jupyter-server's releases.

    v1.15.3

    1.15.3

    (Full Changelog)

    Bugs fixed

    Maintenance and upkeep improvements

    Contributors to this release

    (GitHub contributors page for this release)

    @​blink1073 | @​codecov-commenter | @​minrk

    v1.15.2

    1.15.2

    (Full Changelog)

    Bugs fixed

    Maintenance and upkeep improvements

    Contributors to this release

    (GitHub contributors page for this release)

    @​blink1073 | @​minrk | @​Zsailer

    v1.15.1

    1.15.1

    (Full Changelog)

    ... (truncated)

    Changelog

    Sourced from jupyter-server's changelog.

    Changelog

    All notable changes to this project will be documented in this file.

    1.15.6

    (Full Changelog)

    Bugs fixed

    • Missing warning when no authorizer in found ZMQ handlers #744 (@​Zsailer)

    Maintenance and upkeep improvements

    Contributors to this release

    (GitHub contributors page for this release)

    @​blink1073 | @​codecov-commenter | @​Zsailer

    1.15.5

    (Full Changelog)

    Bugs fixed

    • Relax type checking on ExtensionApp.serverapp #739 (@​minrk)
    • raise no-authorization warning once and allow disabled authorization #738 (@​Zsailer)

    Maintenance and upkeep improvements

    Contributors to this release

    (GitHub contributors page for this release)

    @​blink1073 | @​codecov-commenter | @​minrk | @​Zsailer

    1.15.3

    (Full Changelog)

    ... (truncated)

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    dependencies 
    opened by dependabot[bot] 1
  • chore(deps): Bump ipython from 7.23.0 to 7.31.1

    chore(deps): Bump ipython from 7.23.0 to 7.31.1

    Bumps ipython from 7.23.0 to 7.31.1.

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    dependencies 
    opened by dependabot[bot] 1
  • chore(deps): Bump pillow from 8.2.0 to 9.0.0

    chore(deps): Bump pillow from 8.2.0 to 9.0.0

    Bumps pillow from 8.2.0 to 9.0.0.

    Release notes

    Sourced from pillow's releases.

    9.0.0

    https://pillow.readthedocs.io/en/stable/releasenotes/9.0.0.html

    Changes

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    9.0.0 (2022-01-02)

    • Restrict builtins for ImageMath.eval(). CVE-2022-22817 #5923 [radarhere]

    • Ensure JpegImagePlugin stops at the end of a truncated file #5921 [radarhere]

    • Fixed ImagePath.Path array handling. CVE-2022-22815, CVE-2022-22816 #5920 [radarhere]

    • Remove consecutive duplicate tiles that only differ by their offset #5919 [radarhere]

    • Improved I;16 operations on big endian #5901 [radarhere]

    • Limit quantized palette to number of colors #5879 [radarhere]

    • Fixed palette index for zeroed color in FASTOCTREE quantize #5869 [radarhere]

    • When saving RGBA to GIF, make use of first transparent palette entry #5859 [radarhere]

    • Pass SAMPLEFORMAT to libtiff #5848 [radarhere]

    • Added rounding when converting P and PA #5824 [radarhere]

    • Improved putdata() documentation and data handling #5910 [radarhere]

    • Exclude carriage return in PDF regex to help prevent ReDoS #5912 [hugovk]

    • Fixed freeing pointer in ImageDraw.Outline.transform #5909 [radarhere]

    • Added ImageShow support for xdg-open #5897 [m-shinder, radarhere]

    • Support 16-bit grayscale ImageQt conversion #5856 [cmbruns, radarhere]

    • Convert subsequent GIF frames to RGB or RGBA #5857 [radarhere]

    ... (truncated)

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    dependencies 
    opened by dependabot[bot] 1
  • chore(deps): Bump pillow from 8.2.0 to 8.3.2

    chore(deps): Bump pillow from 8.2.0 to 8.3.2

    Bumps pillow from 8.2.0 to 8.3.2.

    Release notes

    Sourced from pillow's releases.

    8.3.2

    https://pillow.readthedocs.io/en/stable/releasenotes/8.3.2.html

    Security

    • CVE-2021-23437 Raise ValueError if color specifier is too long [hugovk, radarhere]

    • Fix 6-byte OOB read in FliDecode [wiredfool]

    Python 3.10 wheels

    • Add support for Python 3.10 #5569, #5570 [hugovk, radarhere]

    Fixed regressions

    • Ensure TIFF RowsPerStrip is multiple of 8 for JPEG compression #5588 [kmilos, radarhere]

    • Updates for ImagePalette channel order #5599 [radarhere]

    • Hide FriBiDi shim symbols to avoid conflict with real FriBiDi library #5651 [nulano]

    8.3.1

    https://pillow.readthedocs.io/en/stable/releasenotes/8.3.1.html

    Changes

    8.3.0

    https://pillow.readthedocs.io/en/stable/releasenotes/8.3.0.html

    Changes

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    8.3.2 (2021-09-02)

    • CVE-2021-23437 Raise ValueError if color specifier is too long [hugovk, radarhere]

    • Fix 6-byte OOB read in FliDecode [wiredfool]

    • Add support for Python 3.10 #5569, #5570 [hugovk, radarhere]

    • Ensure TIFF RowsPerStrip is multiple of 8 for JPEG compression #5588 [kmilos, radarhere]

    • Updates for ImagePalette channel order #5599 [radarhere]

    • Hide FriBiDi shim symbols to avoid conflict with real FriBiDi library #5651 [nulano]

    8.3.1 (2021-07-06)

    • Catch OSError when checking if fp is sys.stdout #5585 [radarhere]

    • Handle removing orientation from alternate types of EXIF data #5584 [radarhere]

    • Make Image.array take optional dtype argument #5572 [t-vi, radarhere]

    8.3.0 (2021-07-01)

    • Use snprintf instead of sprintf. CVE-2021-34552 #5567 [radarhere]

    • Limit TIFF strip size when saving with LibTIFF #5514 [kmilos]

    • Allow ICNS save on all operating systems #4526 [baletu, radarhere, newpanjing, hugovk]

    • De-zigzag JPEG's DQT when loading; deprecate convert_dict_qtables #4989 [gofr, radarhere]

    • Replaced xml.etree.ElementTree #5565 [radarhere]

    ... (truncated)

    Commits
    • 8013f13 8.3.2 version bump
    • 23c7ca8 Update CHANGES.rst
    • 8450366 Update release notes
    • a0afe89 Update test case
    • 9e08eb8 Raise ValueError if color specifier is too long
    • bd5cf7d FLI tests for Oss-fuzz crash.
    • 94a0cf1 Fix 6-byte OOB read in FliDecode
    • cece64f Add 8.3.2 (2021-09-02) [CI skip]
    • e422386 Add release notes for Pillow 8.3.2
    • 08dcbb8 Pillow 8.3.2 supports Python 3.10 [ci skip]
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • chore(deps): Bump notebook from 6.3.0 to 6.4.1

    chore(deps): Bump notebook from 6.3.0 to 6.4.1

    Bumps notebook from 6.3.0 to 6.4.1.

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    dependencies 
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  • chore(deps): Bump jupyterlab from 3.0.14 to 3.0.17

    chore(deps): Bump jupyterlab from 3.0.14 to 3.0.17

    Bumps jupyterlab from 3.0.14 to 3.0.17.

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    Sourced from jupyterlab's releases.

    v3.0.16

    (Full Changelog)

    Maintenance and upkeep improvements

    Contributors to this release

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    @​blink1073 | @​echarles | @​ian-r-rose | @​jtpio | @​jupyterlab-dev-mode | @​krassowski | @​meeseeksmachine

    v3.0.15

    (Full Changelog)

    Enhancements made

    Maintenance and upkeep improvements

    Documentation improvements

    Other merged PRs

    Contributors to this release

    (GitHub contributors page for this release)

    @​agoose77 | @​blink1073 | @​echarles | @​fperez | @​goanpeca | @​isabela-pf | @​jasongrout | @​jtpio | @​jupyterlab-dev-mode | @​krassowski | @​marthacryan | @​meeseeksmachine | @​mlucool | @​SylvainCorlay | @​welcome

    Changelog

    Sourced from jupyterlab's changelog.


    github_url: 'https://github.com/jupyterlab/jupyterlab/blob/master/CHANGELOG.md'

    JupyterLab Changelog

    4.0

    4.0.0a4

    (Full Changelog)

    Enhancements made

    Bugs fixed

    Maintenance and upkeep improvements

    Documentation improvements

    Contributors to this release

    (GitHub contributors page for this release)

    @​3coins | @​afshin | @​blink1073 | @​fcollonval | @​goanpeca | @​jasongrout | @​JohanMabille | @​jupyterlab-dev-mode | @​krassowski | @​richardkang112 | @​vkaidalov-rft

    4.0.0a3

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    ... (truncated)

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    dependencies 
    opened by dependabot[bot] 1
  • chore(deps): Bump urllib3 from 1.26.4 to 1.26.5

    chore(deps): Bump urllib3 from 1.26.4 to 1.26.5

    Bumps urllib3 from 1.26.4 to 1.26.5.

    Release notes

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    1.26.5

    :warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

    • Fixed deprecation warnings emitted in Python 3.10.
    • Updated vendored six library to 1.16.0.
    • Improved performance of URL parser when splitting the authority component.

    If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors

    Changelog

    Sourced from urllib3's changelog.

    1.26.5 (2021-05-26)

    • Fixed deprecation warnings emitted in Python 3.10.
    • Updated vendored six library to 1.16.0.
    • Improved performance of URL parser when splitting the authority component.
    Commits
    • d161647 Release 1.26.5
    • 2d4a3fe Improve performance of sub-authority splitting in URL
    • 2698537 Update vendored six to 1.16.0
    • 07bed79 Fix deprecation warnings for Python 3.10 ssl module
    • d725a9b Add Python 3.10 to GitHub Actions
    • 339ad34 Use pytest==6.2.4 on Python 3.10+
    • f271c9c Apply latest Black formatting
    • 1884878 [1.26] Properly proxy EOF on the SSLTransport test suite
    • See full diff in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • chore(deps): Bump numpy from 1.20.2 to 1.22.0

    chore(deps): Bump numpy from 1.20.2 to 1.22.0

    Bumps numpy from 1.20.2 to 1.22.0.

    Release notes

    Sourced from numpy's releases.

    v1.22.0

    NumPy 1.22.0 Release Notes

    NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

    • Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.
    • A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.
    • NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.
    • New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.
    • A new configurable allocator for use by downstream projects.

    These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

    The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

    Expired deprecations

    Deprecated numeric style dtype strings have been removed

    Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

    (gh-19539)

    Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

    numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

    (gh-19615)

    ... (truncated)

    Commits

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    dependencies 
    opened by dependabot[bot] 0
  • chore(deps): Bump pillow from 8.2.0 to 9.0.1

    chore(deps): Bump pillow from 8.2.0 to 9.0.1

    Bumps pillow from 8.2.0 to 9.0.1.

    Release notes

    Sourced from pillow's releases.

    9.0.1

    https://pillow.readthedocs.io/en/stable/releasenotes/9.0.1.html

    Changes

    • In show_file, use os.remove to remove temporary images. CVE-2022-24303 #6010 [@​radarhere, @​hugovk]
    • Restrict builtins within lambdas for ImageMath.eval. CVE-2022-22817 #6009 [radarhere]

    9.0.0

    https://pillow.readthedocs.io/en/stable/releasenotes/9.0.0.html

    Changes

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    9.0.1 (2022-02-03)

    • In show_file, use os.remove to remove temporary images. CVE-2022-24303 #6010 [radarhere, hugovk]

    • Restrict builtins within lambdas for ImageMath.eval. CVE-2022-22817 #6009 [radarhere]

    9.0.0 (2022-01-02)

    • Restrict builtins for ImageMath.eval(). CVE-2022-22817 #5923 [radarhere]

    • Ensure JpegImagePlugin stops at the end of a truncated file #5921 [radarhere]

    • Fixed ImagePath.Path array handling. CVE-2022-22815, CVE-2022-22816 #5920 [radarhere]

    • Remove consecutive duplicate tiles that only differ by their offset #5919 [radarhere]

    • Improved I;16 operations on big endian #5901 [radarhere]

    • Limit quantized palette to number of colors #5879 [radarhere]

    • Fixed palette index for zeroed color in FASTOCTREE quantize #5869 [radarhere]

    • When saving RGBA to GIF, make use of first transparent palette entry #5859 [radarhere]

    • Pass SAMPLEFORMAT to libtiff #5848 [radarhere]

    • Added rounding when converting P and PA #5824 [radarhere]

    • Improved putdata() documentation and data handling #5910 [radarhere]

    • Exclude carriage return in PDF regex to help prevent ReDoS #5912 [hugovk]

    • Fixed freeing pointer in ImageDraw.Outline.transform #5909 [radarhere]

    ... (truncated)

    Commits
    • 6deac9e 9.0.1 version bump
    • c04d812 Update CHANGES.rst [ci skip]
    • 4fabec3 Added release notes for 9.0.1
    • 02affaa Added delay after opening image with xdg-open
    • ca0b585 Updated formatting
    • 427221e In show_file, use os.remove to remove temporary images
    • c930be0 Restrict builtins within lambdas for ImageMath.eval
    • 75b69dd Dont need to pin for GHA
    • cd938a7 Autolink CWE numbers with sphinx-issues
    • 2e9c461 Add CVE IDs
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 0
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